Abstract
INTRODUCTION AND OBJECTIVES: Epigenetic changes, including promoter CpG island hypermethylation, occur frequently in bladder cancer (BC) and may be exploited as a means for BC detection and distinction between high-grade (HG) and low-grade (LG) disease. METHODS: To determine epigenetic differences between LG and HG BC we performed genome-wide methylation analysis with Agilent Human CpG Island Microarrays on a panel of fresh frozen BC tissue samples. Using Linear Models for Microarray Data (LIMMA) and local-pooled-error (LPE) approaches and unsupervised hierarchical clustering we identified 990 probes comprising a 32-gene panel that completely distinguished LG from HG BC based on methylation status. We selected five representative differentially methylated genes (DMGs) from our 32-gene panel for methylation validation by real-time PCRbased MethyLight in a series of 40 LG cases ageand sex-matched to 40 HG cases. RESULTS: Among the DMGs tested, including EOMES, GP5, PAX6, TCF4, and ZSCAN12, we identified that EOMES, GP5, and ZSCAN12 methylation significantly differs between normal, LG, and HG disease. GP5 and ZSCAN12, two novel methylated genes in BC, are significantly hypermethylated in HG versus LG BC (p1⁄40.006 and 0.028, respectively). Pathway enrichment analysis and functional annotation determined the most frequently methylated pathways in HG BC were enriched for anterior/posterior pattern specification, embryonic skeletal system development, and neuron fate commitment. The molecular functions of the most enriched genes were involved in DNA binding and transcription factor activity. CONCLUSIONS: These results indicate the ability to distinguish normal tissue from cancer, as well as LG from HG tumours, and reveal important pathways dysregulated in HG BC. Ultimately, the creation of a methylation panel able to distinguish between disease phenotypes will improve disease management and patient outcomes.
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